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The complete chloroplast genome sequence of carmine radish (Raphanus sativus L.) and its evolutionary implications

Jian Gao^a,b, Fabo Chen^a,b, Shumei Shang^a,b, Jun Shu^a, Yi Liu^a, Wenbo Li^a,b,*

 
ABSTRACT:     Carmine radish is well known for its natural red pigment (red radish pigment) and is produced in Chongqing, China. Here, the chloroplast (cp) genome of the local carmine radish cultivar ’Hongxin 1’ was identified through de novo assembly on a third-generation sequencing platform. The results showed that the Hongxin radish cp genome of 153 419 bp consists of four different regions: two inverted repeated regions (IRa and IRb, 26 986 bp each), a large single-copy region (LSC) of 88 448 bp, and a small single-copy region (SSC) of 17 814 bp. In addition, a number of genes (125) were identified, comprising 88 predicted protein-coding genes, 29 tRNA genes and 8 rRNA genes. Compared with the radish cultivar WK10039 cp genome, one predicted protein-coding gene was identified, but 8 tRNA genes were not found in the carmine radish chloroplast genome. Moreover, 12 forward and 14 inverted repeats were identified as well as 58 simple sequence repeats (SSRs). In addition, only slight differences were found between Raphanus sativus (Keroan) and carmine radish (Hongxin), except that ycf15 was only detected in R. sativus (Hongxin). Phylogenetic analysis of the 50 protein-coding genes from the cp genome sequences of 30 Brassicaceae species indicated that R. sativus (Hongxin) is most closely related to Brassica napus and Brassica nigra. This study is the first to generate a valuable resource for SSR marker development studies in carmine radish and provides a basis for further studies on genomics and functional genomics in this type of radish.

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* Corresponding author, E-mail: liverb@163.com

Received 12 Jul 2019, Accepted 16 Jun 2020